Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis in a longitudinal study of three dairy herds

Investigating effective testing strategies for the control of Johne's disease in western Canadian cow-calf herds using an agent-based simulation model

Johne's disease is an insidious infectious disease of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Johne's disease can have important implications for animal welfare and risks causing economic losses in affected herds due to reduced productivity, premature culling and replacement, and veterinary costs. Despite the limited accuracy of diagnostic tools, testing and culling is the primary option for controlling Johne's disease in beef herds. However, evidence to inform specific test and cull strategies is lacking. In this study, a stochastic, continuous-time agent-based model was developed to investigate Johne's disease and potential control options in a typical western Canadian cow-calf herd. The objective of this study was to compare different testing and culling scenarios that included varying the testing method and frequency as well as the number and risk profile of animals targeted for testing using the model. The relative effectiveness of each testing scenario was determined by the simulated prevalence of cattle shedding MAP after a 10-year testing period. A second objective was to compare the direct testing costs of each scenario to identify least-cost options that are the most effective at reducing within-herd disease prevalence. Whole herd testing with individual PCR at frequencies of 6 or 12 months were the most effective options for reducing disease prevalence. Scenarios that were also effective at reducing prevalence but with the lowest total testing costs included testing the whole herd with individual PCR every 24 months and testing the whole herd with pooled PCR every 12 months. The most effective method with the lowest annual testing cost per unit of prevalence reduction was individual PCR on the whole herd every 24 months. Individual PCR testing only cows that had not already been tested 4 times also ranked well when considering both final estimated prevalence at 10 years and cost per unit of gain. A more in-depth economic analysis is needed to compare the cost of testing to the cost of disease, taking into account costs of culling, replacements and impacts on calf crops, and to determine if testing is an economically attractive option for commercial cow-calf operations.

Assessment of the frequency of Mycobacterium bovis shedding in the faeces of naturally and experimentally TB infected cattle

Aims

To assess the prevalence of Mycobacterium bovis bacilli in faecal samples of tuberculous cattle, and to better understand the risk of environmental dissemination of bovine tuberculosis (TB) through the spreading of manure or slurry.

Methods and Results

Faecal samples were collected from 72 naturally infected cattle with visible lesions of TB that had reacted to the tuberculin skin test and 12 cattle experimentally infected with M. bovis. These were examined by microbial culture and PCR to assess the presence of M. bovis bacilli. There were no positive cultures from any naturally infected test reactor animal. A single M. bovis colony was cultured from a faecal sample from one of the experimentally infected animals. A single PCR positive result was obtained from the faecal sample of one naturally infected test reactor.

Conclusions

The prevalence of M. bovis in the faecal samples of TB‐infected cattle was extremely low.

Significance and Impact of the Study

The results suggest that the risk of spreading TB through the use of slurry or manure as an agricultural fertilizer is lower than that suggested in some historical literature. The results could inform a reconsideration of current risk assessments and guidelines on the disposal of manure and slurry from TB‐infected herds.

Comparison of Mycobacterium avium subsp. paratuberculosis infection in cattle, sheep and goats in the Khuzestan Province of Iran: Results of a preliminary survey

Background

Paratuberculosis or Johne's disease, the chronic infectious granulomatous enteritis of ruminants, is a worldwide infection, which is caused by Mycobacterium avium subsp. paratuberculosis (MAP). The most common symptoms of this disease in cattle are loss of milk production, weight loss and diarrhoea, whereas in sheep and goats, the symptoms are emaciation, anorexia and severe disability.

Objectives

The aim of this study was to compare the seroprevalence of MAP in cattle, sheep and goats in the southwest of Iran.

Methods

Blood samples were randomly collected from 530 cattle, 568 sheep and 368 goats in southwest of Iran. Sera were tested by a commercial ELISA kit (ID vet; ID Screen® Paratuberculosis Indirect) for detection of antibodies of MAP.

Results

Overall apparent and true seroprevalence rate of MAP was 6.00% (95% CI: 4.90%–7.30%) and 13.25% (95% CI: 11.55%– 14.95%). Apparent and true seroprevalence of MAP, respectively, was 4.34% (95% CI: 3.88%–6.46%) and 9.19% (95% CI: 6.98%–11.98%) in cattle, 6.87% (95% CI: 5.05%–9.27%) and 15.37% (95% CI: 12.60%–16.60%) in sheep and 7.07% (95% CI: 4.82%–10.18%) and 15.86% (95% CI: 12.41%–20.01%) in goats, respectively. As a result, there was no significant relationship between animal species and MAP infection. Moreover, multivariate logistic regression showed that the infection rate is not associated with age, gender and geographical location in cattle, sheep and goats (P > 0.05).

Conclusion

This study confirms that the seroprevalence of MAP is relatively considerable in the cattle, sheep and goats in the southwest of Iran, although in cattle, it is less than goats and sheep. Therefore, preventive and control measures should be considered by animal health authorities and meat and dairy processing units.

Who infects whom?-Reconstructing infection chains of Mycobacterium avium ssp. paratuberculosis in an endemically infected dairy herd by use of genomic data

Recent evidence of circulation of multiple strains within herds and mixed infections of cows marks the beginning of a rethink of our knowledge on Mycobacterium avium ssp. paratuberculosis (MAP) epidemiology. Strain typing opens new ways to investigate MAP transmission. This work presents a method for reconstructing infection chains in a setting of endemic Johne’s disease on a well-managed dairy farm. By linking genomic data with demographic field data, strain-specific differences in spreading patterns could be quantified for a densely sampled dairy herd. Mixed infections of dairy cows with MAP are common, and some strains spread more successfully. Infected cows remain susceptible for co-infections with other MAP genotypes. The model suggested that cows acquired infection from 1–4 other cows and spread infection to 0–17 individuals. Reconstructed infection chains supported the hypothesis that high shedding animals that started to shed at an early age and showed a progressive infection pattern represented a greater risk for spreading MAP. Transmission of more than one genotype between animals was recorded. In this farm with a good MAP control management program, adult-to-adult contact was proposed as the most important transmission route to explain the reconstructed networks. For each isolate, at least one more likely ancestor could be inferred. Our study results help to capture underlying transmission processes and to understand the challenges of tracing MAP spread within a herd. Only the combination of precise longitudinal field data and bacterial strain type information made it possible to trace infection in such detail.

Evolutionary genomic and bacteria GWAS analysis of Mycobacterium avium subsp. paratuberculosis and dairy cattle Johne's disease phenotypes

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease in ruminants, which has important health consequences for dairy cattle. The Regional Dairy Quality Management Alliance (RDQMA) project is a multistate research program involving MAP isolates taken from three intensively studied commercial dairy farms in the northeastern United States, which emphasized longitudinal data collection of both MAP isolates and animal health in three regional dairy herds for a period of about 7 years. This paper reports the results of a pan-GWAS analysis involving 318 MAP isolates and dairy cow Johne's disease phenotypes, taken from these three farms. Based on our highly curated accessory gene count the pan-GWAS analysis identified several MAP genes associated with bovine Johne's disease phenotypes scored from these three farms, with some of the genes having functions suggestive of possible cause/effect relationships to these phenotypes. This paper reports a pan-genomic comparative analysis between MAP and Mycobacterium tuberculosis, assessing functional Gene Ontology category enrichments between these taxa. Finally, we also provide a population genomic perspective on the effectiveness of herd isolation, involving closed dairy farms, in preventing MAP inter-farm cross infection on a micro-geographic scale.IMPORTANCE Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease in ruminants, which has important health consequences for dairy cattle, and enormous economic consequences for the dairy industry. Understanding which genes in this bacterium are correlated with key disease phenotypes can lead to functional experiments targeting these genes and ultimately lead to improved control strategies. This study represents a rare example of a prolonged longitudinal study of dairy cattle where the disease was measured and the bacteria were isolated from the same cows. The genome sequences of over 300 MAP isolates were analyzed for genes that were correlated with a wide range of Johne's disease phenotypes. A number of genes were identified that were significantly associated with several aspects of the disease and suggestive of further experimental follow-up.

Characterizing infectious disease progression through discrete states using hidden Markov models

Infectious disease management relies on accurate characterization of disease progression so that transmission can be prevented. Slowly progressing infectious diseases can be difficult to characterize because of a latency period between the time an individual is infected and when they show clinical signs of disease. The introduction of Mycobacterium avium ssp. paratuberculosis (MAP), the cause of Johne’s disease, onto a dairy farm could be undetected by farmers for years before any animal shows clinical signs of disease. In this time period infected animals may shed thousands of colony forming units. Parameterizing trajectories through disease states from infection to clinical disease can help farmers to develop control programs based on targeting individual disease state, potentially reducing both transmission and production losses due to disease. We suspect that there are two distinct progression pathways; one where animals progress to a high-shedding disease state, and another where animals maintain a low-level of shedding without clinical disease. We fit continuous-time hidden Markov models to multi-year longitudinal fecal sampling data from three US dairy farms, and estimated model parameters using a modified Baum-Welch expectation maximization algorithm. Using posterior decoding, we observed two distinct shedding patterns: cows that had observations associated with a high-shedding disease state, and cows that did not. This model framework can be employed prospectively to determine which cows are likely to progress to clinical disease and may be applied to characterize disease progression of other slowly progressing infectious diseases.

Characterization of potential superspreader farms for bovine tuberculosis: A review

Background

Variation in host attributes that influence their contact rates and infectiousness can lead some individuals to make disproportionate contributions to the spread of infections. Understanding the roles of such ‘superspreaders’ can be crucial in deciding where to direct disease surveillance and controls to greatest effect. In the epidemiology of bovine tuberculosis (bTB) in Great Britain, it has been suggested that a minority of cattle farms or herds might make disproportionate contributions to the spread of Mycobacterium bovis, and hence might be considered ‘superspreader farms’.

Objectives and Methods

We review the literature to identify the characteristics of farms that have the potential to contribute to exceptional values in the three main components of the farm reproductive number ‐ R_f: contact rate, infectiousness and duration of infectiousness, and therefore might characterize potential superspreader farms for bovine tuberculosis in Great Britain.

Results

Farms exhibit marked heterogeneity in contact rates arising from between‐farm trading of cattle. A minority of farms act as trading hubs that greatly augment connections within cattle trading networks. Herd infectiousness might be increased by high within‐herd transmission or the presence of supershedding individuals, or infectiousness might be prolonged due to undetected infections or by repeated local transmission, via wildlife or fomites.

Conclusions

Targeting control methods on putative superspreader farms might yield disproportionate benefits in controlling endemic bovine tuberculosis in Great Britain. However, real‐time identification of any such farms, and integration of controls with industry practices, present analytical, operational and policy challenges.

Longitudinal study of Mycobacterium avium ssp. paratuberculosis fecal shedding patterns and concurrent serological patterns in naturally infected dairy cattle

Mycobacterium avium ssp. paratuberculosis (MAP) is the etiological agent of paratuberculosis, a disease that affects ruminants worldwide. Despite global interest in the control of this disease, gaps exist in our knowledge of fecal shedding patterns and concurrent serological patterns. This longitudinal study in dairy cattle herds with high MAP seroprevalence in France aimed at accurately describing fecal shedding patterns over 1 year; relating those shedding patterns to individual animal characteristics (age, breed, parity); and exploring the association between fecal shedding patterns and serological patterns. To describe temporal fecal shedding patterns and continuity of shedding, along with the standard quantitative PCR (qPCR) threshold cycle we used a cutoff value that related to low or nonculturable fecal shedding. We also defined a threshold cycle indicative of shedding in high quantities to describe infection progression patterns. Twenty-one herds completed the study, and 782 cows were tested 4 times each. We obtained 4 sets of paired fecal qPCR and serum ELISA results from 757 cows. Although we targeted highly likely infectious animals, we found a large diversity of shedding patterns, as well as high variability between herds in the proportion of animals showing a given pattern. The fecal qPCR results of almost 20% of the final study sample were positioned at least once in the range that indicated low or nonculturable fecal shedding (between the adjusted and the standard cutoff value). Although these animals would typically be classified as non-shedders, they could be important to infection dynamics on the farm. Animals that shed at least twice consecutively and animals that shed in high quantities rarely reverted to negativity. Repeated fecal qPCR can be used to detect temporal fecal shedding traits, and the decision to cull an animal could practically be based on temporal, semiquantitative results. Overall, we found a mismatch between fecal shedding and ELISA seropositivity (637 animals were ELISA-negative 4 times, but only 13% of those animals were qPCR-negative 4 times). We found that having more than 2 ELISA-positive samples was strongly related to persistent and continuous shedding. We suggest that although serological testing is much less sensitive than qPCR, it can also be used, particularly over the course of multiple testing events, to identify animals that are most likely to contribute to the contamination of the farm environment.

Elucidating Transmission Patterns of Endemic Mycobacterium avium subsp. paratuberculosis Using Molecular Epidemiology

Mycobacterial diseases are persistent and characterized by lengthy latent periods. Thus, epidemiological models require careful delineation of transmission routes. Understanding transmission routes will improve the quality and success of control programs. We aimed to study the infection dynamics of Mycobacterium avium subsp. paratuberculosis (MAP), the causal agent of ruminant Johne’s disease, and to distinguish within-host mutation from individual transmission events in a longitudinally MAP-defined dairy herd in upstate New York. To this end, semi-annual fecal samples were obtained from a single dairy herd over the course of seven years, in addition to tissue samples from a selection of culled animals. All samples were cultured for MAP, and multi-locus short-sequence repeat (MLSSR) typing was used to determine MAP SSR types. We concluded from these precise MAP infection data that, when the tissue burden remains low, the majority of MAP infections are not detectable by routine fecal culture but will be identified when tissue culture is performed after slaughter. Additionally, we determined that in this herd vertical infection played only a minor role in MAP transmission. By means of extensive and precise longitudinal data from a single dairy herd, we have come to new insights regarding MAP co-infections and within-host evolution.

A data-driven individual-based model of infectious disease in livestock operation: A validation study for paratuberculosis

Chronic livestock diseases cause large financial loss and affect animal health and welfare. Controlling these diseases mostly requires precise information on both individual animal and population dynamics to inform the farmer’s decisions, but even successful control programmes do by no means assure elimination. Mathematical models provide opportunities to test different control and elimination options rather than implementing them in real herds, but these models require robust parameter estimation and validation. Fitting these models to data is a difficult task due to heterogeneities in livestock processes. In this paper, we develop an infectious disease modeling framework for a livestock disease (paratuberculosis) that is caused by Mycobacterium avium subsp. paratuberculosis (MAP). Infection with MAP leads to reduced milk production, pregnancy rates, and slaughter value and increased culling rates in cattle and causes significant economic losses to the dairy industry. These economic effects are particularly important motivations in the control and elimination of MAP. In this framework, an individual-based model (IBM) of a dairy herd was built and MAP infection dynamics was integrated. Once the model produced realistic dynamics of MAP infection, we implemented an evaluation method by fitting it to data from three dairy herds from the Northeast region of the US. The model fitting exercises used least-squares and parameter space searching methods to obtain the best-fitted values of selected parameters. The best set of parameters were used to model the effect of interventions. The results show that the presented model can complement real herd statistics where the intervention strategies suggest a reduction in MAP prevalence without elimination. Overall, this research not only provides a complete model for MAP infection dynamics in a dairy herd but also offers a method for estimating parameters by fitting IBM models.

Genotyping methods and molecular epidemiology of Mycobacterium avium subsp. paratuberculosis (MAP)

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne’s disease (JD) which affects mainly ruminants and is characterized by chronic diarrhea and emaciation. Johne’s disease is highly prevalent in many countries around the world and leads to high economic losses associated with decreased production. Genotyping of the involved pathogen could be used in the study of population genetics, pathogenesis and molecular epidemiology including disease surveillance and outbreak investigation. Principally, researchers have first assumed the presence of two different MAP strains that are associated with the animal host species (cattle and sheep). However, nowadays MAP characterization depends mainly upon genetic testing using genetic markers such as insertion elements, repetitive sequences and single nucleotide polymorphisms. This work aims to provide an overview of the advances in molecular biological tools used for MAP typing in the last two decades, discuss how these methods have been used to address interesting epidemiological questions, and explore the future prospects of MAP molecular epidemiology given the ever decreasing costs of the high throughput sequencing technology.

Quantifying fecal shedding of Mycobacterium avium ssp. paratuberculosis from calves after experimental infection and exposure

Johne's disease, a chronic enteritis caused by Mycobacterium avium ssp. paratuberculosis (MAP), causes large economic losses to the dairy industry worldwide. Fecal shedding of MAP contaminates the environment, feed, and water and contributes to new infections on farm, yet there is limited knowledge regarding mechanisms of shedding, extent of intermittent shedding, and numbers of MAP bacteria shed. The objectives were to (1) compare (in an experimental setting) the frequency at which intermittent shedding occurred and the quantity of MAP shed among pen mates that were inoculated or contact-exposed (CE); and (2) determine whether an association existed between inoculation dose and quantity of MAP shed. In the first experiment, 32 newborn Holstein-Friesian bull calves were allocated to pens in groups of 4, whereby 2 calves were inoculated with a moderate dose (MD; 5 × 10⁸ cfu) of MAP and 2 calves acted as CE. Calves were group-housed for 3 mo, fecal samples were collected and cultured, and culture-positive samples were quantified. In the second experiment, 6 calves were inoculated with either a low (LD) or high (HD) dose of MAP (1 × 10⁸ or 1 × 10¹⁰ cfu, respectively), and fecal samples were collected for 3 mo and cultured for detection of MAP. The amount of MAP was quantified using direct extraction (DE) of DNA from fecal samples and F57-specific quantitative PCR. In experiment 1, the average amount of MAP in all culture-positive samples did not differ between MD and CE calves. In experiment 2, when comparing inoculation doses, LD calves had the lowest proportion of MAP-positive culture samples and HD had the highest, but no difference was detected in the average quantity of MAP shed. This study provided new information in regards to Johne's disease research and control regarding shedding from various inoculation doses and from CE animals; these data should inform future trials and control programs.

Case definition terminology for paratuberculosis (Johne's disease)

Paratuberculosis (Johne's disease) is an economically significant condition caused by Mycobacterium avium subsp. paratuberculosis. However, difficulties in diagnosis and classification of individual animals with the condition have hampered research and impeded efforts to halt its progressive spread in the global livestock industry. Descriptive terms applied to individual animals and herds such as exposed, infected, diseased, clinical, sub-clinical, infectious and resistant need to be defined so that they can be incorporated consistently into well-understood and reproducible case definitions. These allow for consistent classification of individuals in a population for the purposes of analysis based on accurate counts. The outputs might include the incidence of cases, frequency distributions of the number of cases by age class or more sophisticated analyses involving statistical comparisons of immune responses in vaccine development studies, or gene frequencies or expression data from cases and controls in genomic investigations. It is necessary to have agreed definitions in order to be able to make valid comparisons and meta-analyses of experiments conducted over time by a given researcher, in different laboratories, by different researchers, and in different countries. In this paper, terms are applied systematically in an hierarchical flow chart to enable classification of individual animals. We propose descriptive terms for different stages in the pathogenesis of paratuberculosis to enable their use in different types of studies and to enable an independent assessment of the extent to which accepted definitions for stages of disease have been applied consistently in any given study. This will assist in the general interpretation of data between studies, and will facilitate future meta-analyses.

Which phenotypic traits of resistance should be improved in cattle to control paratuberculosis dynamics in a dairy herd: a modelling approach

Paratuberculosis is a worldwide disease causing production losses in dairy cattle herds. Variability of cattle response to exposure to Mycobacterium avium subsp. paratuberculosis (Map) has been highlighted. Such individual variability could influence Map spread at larger scale. Cattle resistance to paratuberculosis has been shown to be heritable, suggesting genetic selection could enhance disease control. Our objective was to identify which phenotypic traits characterising the individual course of infection influence Map spread in a dairy cattle herd. We used a stochastic mechanistic model. Resistance consisted in the ability to prevent infection and the ability to cope with infection. We assessed the effect of varying (alone and combined) fourteen phenotypic traits characterising the infection course. We calculated four model outputs 25 years after Map introduction in a naïve herd: cumulative incidence, infection persistence, and prevalence of infected and affected animals. A cluster analysis identified influential phenotypes of cattle resistance. An ANOVA quantified the contribution of traits to model output variance. Four phenotypic traits strongly influenced Map spread: the decay in susceptibility with age (the most effective), the quantity of Map shed in faeces by high shedders, the incubation period duration, and the required infectious dose. Interactions contributed up to 12% of output variance, highlighting the expected added-value of improving several traits simultaneously. Combinations of the four most influential traits decreased incidence to less than one newly infected animal per year in most scenarios. Future genetic selection should aim at improving simultaneously the most influential traits to reduce Map spread in cattle populations.

Knowledge gaps that hamper prevention and control of Mycobacterium avium subspecies paratuberculosis infection

In the last decades, many regional and country-wide control programmes for Johne's disease (JD) were developed due to associated economic losses, or because of a possible association with Crohn's disease. These control programmes were often not successful, partly because management protocols were not followed, including the introduction of infected replacement cattle, because tests to identify infected animals were unreliable, and uptake by farmers was not high enough because of a perceived low return on investment. In the absence of a cure or effective commercial vaccines, control of JD is currently primarily based on herd management strategies to avoid infection of cattle and restrict within-farm and farm-to-farm transmission. Although JD control programmes have been implemented in most developed countries, lessons learned from JD prevention and control programmes are underreported. Also, JD control programmes are typically evaluated in a limited number of herds and the duration of the study is less than 5 year, making it difficult to adequately assess the efficacy of control programmes. In this manuscript, we identify the most important gaps in knowledge hampering JD prevention and control programmes, including vaccination and diagnostics. Secondly, we discuss directions that research should take to address those knowledge gaps.

Reducing Foodborne Pathogen Persistence and Transmission in Animal Production Environments: Challenges and Opportunities

Preharvest strategies to reduce zoonotic pathogens in food animals are important components of the farm-to-table food safety continuum. The problem is complex; there are multiple pathogens of concern, multiple animal species under different production and management systems, and a variety of sources of pathogens, including other livestock and domestic animals, wild animals and birds, insects, water, and feed. Preharvest food safety research has identified a number of intervention strategies, including probiotics, direct-fed microbials, competitive exclusion cultures, vaccines, and bacteriophages, in addition to factors that can impact pathogens on-farm, such as seasonality, production systems, diet, and dietary additives. Moreover, this work has revealed both challenges and opportunities for reducing pathogens in food animals. Animals that shed high levels of pathogens and predominant pathogen strains that exhibit long-term persistence appear to play significant roles in maintaining the prevalence of pathogens in animals and their production environment. Continued investigation and advancements in sequencing and other technologies are expected to reveal the mechanisms that result in super-shedding and persistence, in addition to increasing the prospects for selection of pathogen-resistant food animals and understanding of the microbial ecology of the gastrointestinal tract with regard to zoonotic pathogen colonization. It is likely that this continued research will reveal other challenges, which may further indicate potential targets or critical control points for pathogen reduction in livestock. Additional benefits of the preharvest reduction of pathogens in food animals are the reduction of produce, water, and environmental contamination, and thereby lower risk for human illnesses linked to these sources.

Economic consequences of paratuberculosis control in dairy cattle: A stochastic modeling study

The cost of paratuberculosis to dairy herds, through decreased milk production, early culling, and poor reproductive performance, has been well-studied. The benefit of control programs, however, has been debated. A recent stochastic compartmental model for paratuberculosis transmission in US dairy herds was modified to predict herd net present value (NPV) over 25 years in herds of 100 and 1000 dairy cattle with endemic paratuberculosis at initial prevalence of 10% and 20%. Control programs were designed by combining 5 tests (none, fecal culture, ELISA, PCR, or calf testing), 3 test-related culling strategies (all test-positive, high-positive, or repeated positive), 2 test frequencies (annual and biannual), 3 hygiene levels (standard, moderate, or improved), and 2 cessation decisions (testing ceased after 5 negative whole-herd tests or testing continued). Stochastic dominance was determined for each herd scenario; no control program was fully dominant for maximizing herd NPV in any scenario. Use of the ELISA test was generally preferred in all scenarios, but no paratuberculosis control was highly preferred for the small herd with 10% initial prevalence and was frequently preferred in other herd scenarios. Based on their effect on paratuberculosis alone, hygiene improvements were not found to be as cost-effective as test-and-cull strategies in most circumstances. Global sensitivity analysis found that economic parameters, such as the price of milk, had more influence on NPV than control program-related parameters. We conclude that paratuberculosis control can be cost effective, and multiple control programs can be applied for equivalent economic results.

An intra-laboratory cultural and real-time PCR method comparison and evaluation for the detection of subclinical paratuberculosis in dairy herds

Mycobacterium avium subsp. paratuberculosis (MAP) is a vigorous microorganism which causes incurable chronic enteritis, Johne's disease (JD) in cattle. A target of control programmes for JD is to accurately detect MAP-infected cattle early to reduce disease transmission. The present study evaluated the efficacy of two different cultural procedures and a TaqMan real-time PCR assay for detection of subclinical paratuberculosis in dairy herds. Therefore, sixty-one faecal samples were collected from two Dutch dairy herds (n = 40 and n = 21, respectively) which were known to be MAP-ELISA positive. All individual samples were assessed using two different cultural protocols in two different laboratories. The first cultural protocol (first laboratory) included a decontamination step with 0.75% hexadecylpyridinium chloride (HPC) followed by inoculation on Herrold's egg yolk media (HEYM). The second protocol (second laboratory) comprised of a decontamination step using 4% NaOH and malachite green-oxalic acid followed by inoculation on two media, HEYM and in parallel on modified Löwenstein-Jensen media (mLJ). For the TaqMan real-time PCR assay, all faecal samples were tested in two different laboratories using TaqMan® MAP (Johne's) reagents (Life Technologies). The cultural procedures revealed positive reactions in 1.64% of the samples for cultivation protocol 1 and 6.56 and 8.20% of the samples for cultivation protocol 2, respectively. The results of the TaqMan real-time PCR performed in two different laboratories yielded 13.11 and 19.76% positive reaction. The kappa test showed proportional agreement 0.54 between the mLJ media (second laboratory) and TaqMan® real-time PCR method (second laboratory). In conclusion, the TaqMan real-time PCR could be a strongly useful and efficient assay for the detection of subclinical paratuberculosis in dairy cattle leading to an improvement in the efficiency of MAP control strategies.

Merging DNA typing and network analysis to assess the transmission of paratuberculosis between farms

Paratuberculosis, a chronic enteric infection caused by Mycobacterium subsp. paratuberculosis (MAP), is endemic in all farmed ruminant species in New Zealand. The use of genotyping in combination with network analysis of livestock movement events from one farm location to another has the potential to contribute to our understanding of between-farm transmission events. We studied a population of 122 farms from a corporate commercial livestock enterprise in New Zealand, trading with each other in near isolation from other commercial farms. The data consisted of longitudinal movements to and from these farms between 2006 and 2010, as well as the results of cross-sectional MAP screening and genotyping performed in 2010. We explored associations between past livestock movements and current strain type distribution in this population of farms using quadratic assignment procedure. Our results show that measures of farm clustering within the movement network were significantly associated with sharing of MAP strains. For example, farms closely related by trade were twice as likely to share the same strains of MAP (p=0.033). Other covariates were also associated with the probability of sharing the same strains of MAP, such as being located on the same island (OR=5.8 to 8.7, p<0.01), farming the same livestock species and Euclidian distance between farms. The novel approach we used supports the hypothesis that livestock movement is indeed a significant contributor to farm-to-farm transmission of MAP.

A longitudinal study of the Mycobacterium avium subspecies paratuberculosis infection status in young goats and their mothers

The dynamics between Mycobacterium avium subspecies paratuberculosis (MAP) infection and the immune response of goats naturally exposed to MAP were studied in a herd where the clinical expression of paratuberculosis had been observed. Four generations of goats were observed over a 33-month period: mothers of three different generations (G1, G2, G3) and their daughters, generation 4 (G4). A MAP infection status was defined according to the combined results of an IFN-γ assay, antibody response, faecal culture and post-mortem examination. Goats were defined as non-infected (NI), infected and non-shedder (INS), infected and shedder (IS) or atypical (A). Twenty-nine percent of goats were NI, 66% were infected and either shedding (14%) or not shedding (52%) MAP, and 5% were atypical. IFN-γ responses were detected first, followed by faecal shedding and antibody responses. The results showed that in goats naturally exposed to MAP, IFN-γ responses were regularly detected earlier in non-shedders than in young infected shedder goats and were stronger in shedder than in non-shedder goats. They were also higher in the mother goats than in their daughters. Goats shedding MAP or with positive antibody response at the beginning of their pregnancy are more likely to have an infected daughter positive to an IFN-γ assay by the age of 15 months.

Relative frequency of 4 major strain types of Mycobacterium avium ssp. paratuberculosis in Canadian dairy herds using a novel single nucleotide polymorphism-based polymerase chain reaction

Johne's disease is a worldwide concern, as it causes huge economic losses. The etiological agent, Mycobacterium avium ssp. paratuberculosis (MAP), has limited genetic diversity, impeding efforts to understand transmission and distribution of strain types. Whole-genome sequencing was previously performed on a representative set of MAP isolates from Canadian dairy herds and 9 divergent clades were identified. Four clades were of particular interest, as they were either MAP types rarely reported in North America, or they represented a substantial proportion of isolates recovered from dairy farms in Canada. One clade included type I/III isolates, whereas the remaining clades included type II isolates. Variant sites in the MAP genome are often separated by thousands of base pairs, limiting use of single nucleotide polymorphism (SNP)-based genotyping on a single genomic region. Therefore, a SNP-PCR assay was developed to facilitate interrogation of 5 SNP in 2 distant regions of the genome, linking them together in a single PCR reaction for subsequent Sanger sequencing. This high-throughput assay enabled discrimination of 602 MAP isolates from 264 herds (from all 10 provinces). More than 1 isolate was cultured from 133 herds, 14 of which included multiple subtypes. A previously identified dominant type included 87% of isolates, whereas the Bison type was more widespread than previously reported. The latter type and isolates from a second clade of interest were overrepresented in Québec and Saskatchewan, respectively. In conclusion, the distribution and relative frequency of MAP subtypes within Canadian dairy herds were assessed using a novel SNP-based typing assay. These findings will contribute to understanding the clinical relevance and transmission dynamics of MAP in this population and elsewhere.

A novel multilocus variable number tandem repeat analysis typing scheme for African phylotype III strains of the Ralstonia solanacearum species complex

Background. Reliable genotyping that provides an accurate description of diversity in the context of pathogen emergence is required for the establishment of strategies to improve disease management. MultiLocus variable number tandem repeat analysis (MLVA) is a valuable genotyping method. It can be performed at small evolutionary scales where high discriminatory power is needed. Strains of the Ralstonia solanacearum species complex (RSSC) are highly genetically diverse. These destructive pathogens are the causative agent of bacterial wilt on an unusually broad range of host plants worldwide. In this study, we developed an MLVA scheme for genotyping the African RSSC phylotype III. Methods. We selected different publicly available tandem repeat (TR) loci and additional TR loci from the genome of strain CMR15 as markers. Based on these loci, a new phylotype III-MLVA scheme is presented. MLVA and multiLocus sequence typing (MLST) were compared at the global, regional, and local scales. Different populations of epidemiologically related and unrelated RSSC phylotype III strains were used. Results and Discussion. Sixteen polymorphic TR loci, which included seven microsatellites and nine minisatellites, were selected. These TR loci were distributed throughout the genome (chromosome and megaplasmid) and located in both coding and intergenic regions. The newly developed RS3-MLVA16 scheme was more discriminative than MLST. RS3-MLVA16 showed good ability in differentiating strains at global, regional, and local scales, and it especially highlighted epidemiological links between closely related strains at the local scale. RS3-MLVA16 also underlines genetic variability within the same MLST-type and clonal complex, and gives a first overview of population structure. Overall, RS3-MLVA16 is a promising genotyping method for outbreak investigation at a fine scale, and it could be used for outbreak investigation as a first-line, low-cost assay for the routine screening of RSSC phylotype III.

Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection

The molecular regulatory mechanisms of host responses to Mycobacterium avium subsp. paratuberculosis (MAP) infection during the early subclinical stage are still not clear. In this study, surgically isolated ileal segments in newborn calves (n = 5) were used to establish in vivo MAP infection adjacent to an uninfected control intestinal compartment. RNA-Seq was used to profile the whole transcriptome (mRNAs) and the microRNAome (miRNAs) of ileal tissues collected at one-month post-infection. The most related function of the differentially expressed mRNAs between infected and uninfected tissues was “proliferation of endothelial cells”, indicating that MAP infection may lead to the over-proliferation of endothelial cells. In addition, 46.2% of detected mRNAs displayed alternative splicing events. The pre-mRNA of two genes related to macrophage maturation (monocyte to macrophage differentiation-associated) and lysosome function (adenosine deaminase) showed differential alternative splicing events, suggesting that specific changes in the pre-mRNA splicing sites may be a mechanism by which MAP escapes host immune responses. Moreover, 9 miRNAs were differentially expressed after MAP infection. The integrated analysis of microRNAome and transcriptome revealed that these miRNAs might regulate host responses to MAP infection, such as “proliferation of endothelial cells” (bta-miR-196 b), “bacteria recognition” (bta-miR-146 b), and “regulation of the inflammatory response” (bta-miR-146 b).

Impact of the shedding level on transmission of persistent infections in Mycobacterium avium subspecies paratuberculosis (MAP)

Super-shedders are infectious individuals that contribute a disproportionate amount of infectious pathogen load to the environment. A super-shedder host may produce up to 10,000 times more pathogens than other infectious hosts. Super-shedders have been reported for multiple human and animal diseases. If their contribution to infection dynamics was linear to the pathogen load, they would dominate infection dynamics. We here focus on quantifying the effect of super-shedders on the spread of infection in natural environments to test if such an effect actually occurs in Mycobacterium avium subspecies paratuberculosis (MAP). We study a case where the infection dynamics and the bacterial load shed by each host at every point in time are known. Using a maximum likelihood approach, we estimate the parameters of a model with multiple transmission routes, including direct contact, indirect contact and a background infection risk. We use longitudinal data from persistent infections (MAP), where infectious individuals have a wide distribution of infectious loads, ranging upward of three orders of magnitude. We show based on these parameters that the effect of super-shedders for MAP is limited and that the effect of the individual bacterial load is limited and the relationship between bacterial load and the infectiousness is highly concave. A 1000-fold increase in the bacterial contribution is equivalent to up to a 2-3 fold increase in infectiousness.

A new compartmental model of Mycobacterium avium subsp. paratuberculosis infection dynamics in cattle

Models of Mycobacterium avium subsp. paratuberculosis (MAP), a chronic infectious agent of cattle, are used to identify effective control programs. However, new biological findings show that adult infections occur and that infected animals can be separated into 2 paths: animals that will become high-shedding and, eventually, experience clinical disease (high-path); and animals that will shed only small quantities of MAP and will remain subclinical (low-path). Longitudinal data analysis found that high-path animals progress more quickly than previously believed. A standard model of MAP transmission in dairy herds was modified to include adult low-path infections and 2 infection pathways for infected calves. Analysis of this model showed that adult infection may play an important role in MAP dynamics on a dairy farm, and that the increased rate of progression for high-path animals influences both the prevalence and the persistence of MAP on a dairy farm. This new model will be able to determine the effectiveness of MAP control programs more accurately than previous models.

Sensitivity and specificity of repeated test results from a commercial milk enzyme-linked immunosorbent assay for detection of Mycobacterium avium subspecies paratuberculosis in dairy cattle

OBJECTIVE

To investigate the sensitivity and specificity of results of initial and repeated milk ELISAs (at 6- or 12-month intervals) to detect cows that were shedding Mycobacterium avium subsp paratuberculosis (ie, were infectious) and to evaluate factors influencing the probability that the results of a repeated milk ELISA would be positive for an infectious cow if the results of the initial milk ELISA were negative.

DESIGN

Prospective cohort study.

ANIMALS

3,145 dairy cows from 32 herds.

PROCEDURES

Herds from the 3 Maritime provinces in Canada (Prince Edward Island, New Brunswick, and Nova Scotia), participating in a Dairy Herd Improvement program, and that had undergone a prior Mycobacterium avium subsp paratuberculosis awareness project were selected for the study. Sample collection occurred between April 2009 and March 2011 with milk and fecal samples collected from all lactating cows in study herds every 6 months. Herds completing < 3 herd visits with collection of individual cow fecal or milk samples, within this sampling timeframe, were excluded from analyses. Fecal samples were cultured in liquid medium and a cow was defined as infectious if ≥ 1 sample was culture positive (reference test). A milk ELISA (index test) was completed with a commercial kit, following manufacturer's instructions.

RESULTS

For a 6-month test interval, sensitivities of the milk ELISA to detect infectious cows were 22.0% and 32.6% for initial and combined initial and repeated tests (parallel interpretation), respectively. Specificity of the initial ELISA was 99.6% and was 99.2% for combined tests. For a 12-month test interval, sensitivities of the milk ELISA to detect infectious cows were 25.6% and 45.3% for initial and combined initial and repeated tests (parallel interpretation), respectively. Specificity of the initial ELISA was 99.6% and was 98.9% for combined tests. In infectious cows, magnitude of the initial negative ELISA result was a positive predictor for a positive repeated ELISA result.

CONCLUSIONS AND CLINICAL RELEVANCE

Results of a repeated milk ELISA improved detection of Mycobacterium avium subsp paratuberculosis infectious cows, with minimal loss of specificity. A 12-month test interval provided a greater increase in sensitivity, relative to an initial test, than did a 6-month interval. Infectious cows with an initial negative milk ELISA result close to the cutoff for a positive test were more likely to have positive results on a repeated ELISA. Repeated testing improved detection of infectious cows and reduced risk of misclassification compared with a single ELISA result.

Differences in intermittent and continuous fecal shedding patterns between natural and experimental Mycobacterium avium subspecies paratuberculosis infections in cattle

The objective of this paper is to study shedding patterns of cows infected with Mycobacterium avium subsp. paratuberculosis (MAP). While multiple single farm studies of MAP dynamics were reported, there is not large scale meta-analysis of both natural and experimental infections. Large difference in shedding patterns between experimentally and naturally infected cows were observed. Experimental infections are thus probably driven by different pathological mechanisms. For further evaluations of shedding patterns only natural infections were used. Within such infections, the transition to high shedding was studied as a proxy to the development of a clinical disease. The majority of studied cows never developed high shedding levels. Those that do, typically never reduced their shedding level to low or no shedding. Cows that eventually became high shedders showed a pattern of continuous shedding. In contrast, cows with an intermittent shedding pattern had a low probability to ever become high shedders. In addition, cows that start shedding at a younger age (less than three years of age) have a lower hazard of becoming high shedders compared to cows starting to shed at an older age. These data suggest the presence of three categories of immune control. Cows that are intermittent shedders have the infection process under control (no progressive infection). Cows that start shedding persistently at a young age partially control the infection, but eventually will be high shedders (slow progressive infection), while cows that start shedding persistently at an older age cannot effectively control the infection and become high shedders rapidly.

Longitudinal data collection of Mycobacterium avium subspecies Paratuberculosis infections in dairy herds: the value of precise field data

Longitudinal infection data on Mycobacterium avium subspecies paratuberculosis (MAP) was collected on three dairy farms in Northeastern United States during approximately 10 years. Precise data on animal characteristics and animal location within farm were collected on these farms. Cows were followed over time with regard to MAP status during biannual fecal and serum sampling and quarterly serum sampling. Approximately 13 000 serum samples, 6500 fecal samples and 2000 tissue samples were collected during these years. Prevalence of positive samples was 1.4% for serological samples, 2.2% in fecal samples and 16.7% in tissue samples. Infection dynamics of MAP was studied and resulted in a number of potential changes in our understanding of MAP infection dynamics. First, a high prevalence of MAP infection was observed in these herds due to lifetime follow up of cows, including slaughter. Second, two distinctly different infection patterns were observed, so called non-progressors and progressors. Non-progressors were characterized by intermittent and low shedding of MAP bacteria and a virtual absence of a humoral immune response. Progressors were characterized by continuous and progressive shedding and a clearly detectable and progressive humoral immune response. Strain typing of MAP isolates on the three farms identified on two of three farms a dominant strain type, indicating that some strains are more successful in terms of transmission and infection progression. Continuous high quality longitudinal data collection turned out to be an essential tool in our understanding of pathobiology and epidemiology of MAP infections in dairy herds.

Two state model for a constant disease hazard in paratuberculosis (and other bovine diseases)

Many diseases are characterized by a long and varying sub-clinical period. Two main mechanisms can explain such periods: a slow progress toward disease or a sudden transition from a healthy state to a disease state induced by internal or external events. We here survey epidemiological features of the amount of bacteria shed during Mycobacterium Avium Paratuberculosis (MAP) infection to test which of these two models, slow progression or sudden transition (or a combination of the two), better explains the transition from intermittent and low shedding to high shedding. Often, but not always, high shedding is associated with the occurrence of clinical signs. In the case of MAP, the clinical signs include diarrhea, low milk production, poor fertility and eventually emaciation and death. We propose a generic model containing bacterial growth, immune control and fluctuations. This proposed generic model can represent the two hypothesized types of transitions in different parameter regimes. The results show that the sudden transition model provides a simpler explanation of the data, but also suffers from some limitations. We discuss the different immunological mechanism that can explain and support the sudden transition model and the interpretation of each term in the studied model. These conclusions are applicable to a wide variety of diseases, and MAP serves as a good test case based on the large scale measurements of single cow longitudinal profiles in this disease.

A high-morbidity outbreak of Johne's disease in game-ranched elk

Following an outbreak of Johne's disease on an elk farm in northern Alberta, Canada, fecal culture, fecal polymerase chain reaction (PCR), and serum enzyme-linked immunosorbent assay (ELISA) tests were performed on individual animals. The magnitude of the outbreak is described and the challenges associated with poor test agreement, as well as herd management options, are discussed.

Typing of Mycobacterium avium subspecies paratuberculosis isolates from Newfoundland using fragment analysis

Short Sequence Repeat (SSR) typing of Mycobacterium avium subspecies paratuberculosis (Map) isolates is one of the most commonly used method for genotyping this pathogen. Currently used techniques have challenges in analyzing mononucleotide repeats >15 bp, which include some of the Map SSRs. Fragment analysis is a relatively simple technique, which can accurately measure the size of DNA fragments and can be used to calculate the repeat length of the target SSR loci. In the present study, fragment analysis was used to analyze 4 Map SSR loci known to provide sufficient discriminatory power to determine the relationship between Map isolates. Eighty-five Map isolates from 18 animals from the island of Newfoundland were successfully genotyped using fragment analysis. To the best of our knowledge, this is the first report on Map SSR diversity from Newfoundland dairy farms. Previously unreported Map SSR-types or combinations were also identified during the course of the described work. In addition, multiple Map SSR-types were isolated from a single animal in many cases, which is not a common finding.

Ecology and genomic features of infection with Mycobacterium avium subspecies paratuberculosis in Egypt

Mycobacterium avium subspecies paratuberculosis (M. paratuberculosis) is the causative agent of paratuberculosis, or Johne's disease, in cattle, with potential involvement in cases of Crohn's disease in humans. Johne's disease is found worldwide and is economically important for both beef and dairy industries. In an effort to characterize this important infection in Egypt, we analysed the ecological and genomic features of recent isolates of M. paratuberculosis. In this report, we examined 26 Holstein dairy herds distributed throughout Egypt, from 2010 to 2013. Using PCR analysis of faecal samples, we estimated a mean herd-level prevalence of 65.4 %, with animal-level infection that reached a mean of 13.6 % among animals suffering from diarrhoea. Whole genome sequencing of field isolates identified numerous single nucleotide polymorphisms among field isolates relative to the standard M. paratuberculosis K10 genome. Interestingly, the virulence of M. paratuberculosis isolates from Egypt revealed diverse virulence phenotypes in the murine model of paratuberculosis, with significant differences in tissue colonization, particularly during the chronic stage of infection. Overall, our analysis confirmed that Johne's disease is a newly identified problem in Egypt and indicated that M. paratuberculosis has potentially diverse genotypes that impact its virulence. Further ecological mapping and genomic analysis of M. paratuberculosis will enhance our understanding of the transmission and evolutionary dynamics of this pathogen under natural field conditions.

Back to the real world: connecting models with data

Mathematical models for infectious disease are often used to improve our understanding of infection biology or to evaluate the potential efficacy of intervention programs. Here, we develop a mathematical model that aims to describe infection dynamics of Mycobacterium avium subspecies paratuberculosis (MAP). The model was developed using current knowledge of infection biology and also includes some components of MAP infection dynamics that are currently still hypothetical. The objective was to show methods for parameter estimation of state transition models and to connect simulation models with detailed real life data. Thereby making model predictions and results of simulations more reflective and predictive of real world situations. Longitudinal field data from a large observational study are used to estimate parameter values. It is shown that precise data, including molecular diagnostics on the obtained MAP strains, results in more precise and realistic parameter estimates. It is argued that modeling of infection disease dynamics is of great value to understand the patho-biology, epidemiology and control of infectious diseases. The quality of conclusions drawn from model studies depend on two key issues; first, the quality of biology that has gone in the process of developing the model structure; second the quality of the data that go into the estimation of the parameters and the quality and quantity of the data that go into model validation. The more real world data that are used in the model building process, the more likely that modeling studies will provide novel, innovative and valid results.

Molecular epidemiology of Mycobacterium avium subsp. paratuberculosis isolated from sheep, cattle and deer on New Zealand pastoral farms

The present study aimed to describe the molecular diversity of Mycobacterium avium subsp. paratuberculosis (MAP) isolates obtained from sheep, cattle (beef and dairy) and deer farms in New Zealand. A total of 206 independent MAP isolates (15 beef cattle, 89 dairy cattle, 35 deer, 67 sheep) were sourced from 172 species-mobs (15 beef cattle, 66 dairy cattle, 31 deer, 60 sheep). Seventeen subtypes were identified, using a combination of variable number of tandem repeats (VNTR) and short sequence repeat (SSR) methods. Rarefaction analysis, analysis of molecular variance (AMOVA), Fst pairwise comparisons and proportional similarity index (PSI) were used to describe subtype population richness, genetic structure and potential associations between livestock sectors and New Zealand two main islands (North and South). The rarefaction analysis suggests a significantly higher subtype richness in dairy cattle herds when compared to the other livestock sectors. AMOVA results indicate that the main source of subtype variation is attributable to the livestock sector from which samples were sourced suggesting that subtypes are generally sector-specific. The pairwise Fst results were similar, with low Fst values for island differences within a livestock sector when compared to between sector analyses, representing a low subtype differentiation between islands. However, for a given island, potential associations were seen between dominant subtypes and specific livestock sectors. Three subtypes accounted for 76% of the isolates. The most common of these was isolated from sheep and beef cattle in the North Island, the second most frequent subtype was mainly isolated from dairy cattle (either island), while the third most common subtype was associated with deer farmed in the South Island. The PSI analysis suggests similarities in subtypes sourced from sheep and beef cattle. This contrasted with the isolates sourced from other livestock sectors, which tended to present sector-specific subtypes. Sheep and beef cattle were mainly infected with MAP Type I, while dairy cattle and deer were almost exclusively infected with MAP Type II. However, when beef cattle and deer were both present at farm level, they harboured similar subtypes. This study indicates that cross-species transmission of MAP occurs on New Zealand farms although close contact between species appears to be required, as in the case of sheep and beef cattle which are commonly grazed together in New Zealand.

A rational framework for evaluating the next generation of vaccines against Mycobacterium avium subspecies paratuberculosis

Since the early 1980s, several investigations have focused on developing a vaccine against Mycobacterium avium subspecies paratuberculosis (MAP), the causative agent of Johne's disease in cattle and sheep. These studies used whole-cell inactivated vaccines that have proven useful in limiting disease progression, but have not prevented infection. In contrast, modified live vaccines that invoke a Th1 type immune response, may improve protection against infection. Spurred by recent advances in the ability to create defined knockouts in MAP, several independent laboratories have developed modified live vaccine candidates by transpositional mutation of virulence and metabolic genes in MAP. In order to accelerate the process of identification and comparative evaluation of the most promising modified live MAP vaccine candidates, members of a multi-institutional USDA-funded research consortium, the Johne's disease integrated program (JDIP), met to establish a standardized testing platform using agreed upon protocols. A total of 22 candidates vaccine strains developed in five independent laboratories in the United States and New Zealand voluntarily entered into a double blind stage gated trial pipeline. In Phase I, the survival characteristics of each candidate were determined in bovine macrophages. Attenuated strains moved to Phase II, where tissue colonization of C57/BL6 mice were evaluated in a challenge model. In Phase III, five promising candidates from Phase I and II were evaluated for their ability to reduce fecal shedding, tissue colonization and pathology in a baby goat challenge model. Formation of a multi-institutional consortium for vaccine strain evaluation has revealed insights for the implementation of vaccine trials for Johne's disease and other animal pathogens. We conclude by suggesting the best way forward based on this 3-phase trial experience and challenge the rationale for use of a macrophage-to-mouse-to native host pipeline for MAP vaccine development.

Genetic structure of Mycobacterium avium subsp. paratuberculosis population in cattle herds in Quebec as revealed by using a combination of multilocus genomic analyses

Mycobacterium avium subsp. paratuberculosis is the etiological agent of paratuberculosis, a granulomatous enteritis affecting a wide range of domestic and wild ruminants worldwide. A variety of molecular typing tools are used to distinguish M. avium subsp. paratuberculosis strains, contributing to a better understanding of M. avium subsp. paratuberculosis epidemiology. In the present study, PCR-based typing methods, including mycobacterial interspersed repetitive units/variable-number tandem repeats (MIRU-VNTR) and small sequence repeats (SSR) in addition to IS1311 PCR-restriction enzyme analysis (PCR-REA), were used to investigate the genetic heterogeneity of 200 M. avium subsp. paratuberculosis strains from dairy herds located in the province of Quebec, Canada. The majority of strains were of the "cattle type," or type II, although 3 strains were of the "bison type." A total of 38 genotypes, including a novel one, were identified using a combination of 17 genetic markers, which generated a Simpson's index of genetic diversity of 0.876. Additional analyses revealed no differences in genetic diversity between environmental and individual strains. Of note, a spatial and spatiotemporal cluster was evidenced regarding the distribution of one of the most common genotypes. The population had an overall homogeneous genetic structure, although a few strains stemmed out of the consensus cluster, including the bison-type strains. The genetic structure of M. avium subsp. paratuberculosis populations within most herds suggested intraherd dissemination and microevolution, although evidence of interherd contamination was also revealed. The level of genetic diversity obtained by combining MIRU-VNTR and SSR markers shows a promising avenue for molecular epidemiology investigations of M. avium subsp. paratuberculosis transmission patterns.

Evidence of passive faecal shedding of Mycobacterium avium subsp. paratuberculosis in a Limousin cattle herd

It has been suggested that passive shedding of Mycobacterium avium subsp. paratuberculosis (MAP) in faeces may occur, but reliable data are missing. Passive shedding assumes the ingestion of MAP in contaminated feed and passive passage through the gastrointestinal tract without causing infection. In this study the presence of MAP in faeces in a closed herd of Limousin cattle was monitored for 53 months using quantitative real time PCR (qPCR) and culture. The initial prevalence of MAP in the herd was determined to be 63.4% and 4.9% using qPCR and culture, respectively. After the removal of two culture- and qPCR-positive (>10(4) MAP cells/g) cows, the prevalence of MAP using qPCR decreased to 42.1% and later to 15.6% and 6.7%. The continuous removal of suspected animals from the herd during the monitoring period minimised the presence of MAP in faeces to sporadic, which may have resulted from a decrease in the environmental infectious pressure. The findings suggest that the presence of low numbers of MAP in bovine faeces may not necessarily be caused by real infection, but rather by passive passage of MAP. This phenomenon should therefore be considered when interpreting MAP qPCR data.

No holes barred: invasion of the intestinal mucosa by Mycobacterium avium subsp. paratuberculosis

The infection biology of Mycobacterium avium subsp. paratuberculosis has recently crystallized, with added details surrounding intestinal invasion. The involvement of pathogen-derived effector proteins such as the major membrane protein, oxidoreductase, and fibronectin attachment proteins have been uncovered. Mutations constructed in this pathogen have also shed light on genes needed for invasion. The host cell types that are susceptible to invasion have been defined, along with their transcriptional response. Recent details have given a new appreciation for the dynamic interplay between the host and bacterium that occurs at the outset of infection. An initial look at the global expression pathways of the host has shown a circumvention of the cell communication pathway by M. avium subsp. paratuberculosis, which loosens the integrity of the tight junctions. We now know that M. avium subsp. paratuberculosis activates the epithelial layer and also actively recruits macrophages to the site of infection. These notable findings are summarized along with added mechanistic details of the early infection model. We conclude by proposing critical next steps to further elucidate the process of M. avium subsp. paratuberculosis invasion.

How does a Mycobacterium change its spots? Applying molecular tools to track diverse strains of Mycobacterium avium subspecies paratuberculosis

Defining genetic diversity in the wake of the release of several Mycobacterium avium subsp. paratuberculosis (MAP) genome sequences has become a major emphasis in the molecular biology and epidemiology of Johne's disease research. These data can now be used to define the extent of strain diversity on the farm. However, to perform these important tasks, researchers must have a way to distinguish the many MAP isolates/strains that are present in the environment or host to enable tracking over time. Recent studies have described genetic diversity of the Mycobacterium avium complex (MAC), of which MAP is a member, through pulsed-field gel electrophoresis, single sequence repeats, variable-number tandem repeats, genome rearrangements, single nucleotide polymorphisms and genomewide comparisons to identify insertions and deletions. Combinations of these methods can now provide discrimination sufficient for dependable strain tracking. These molecular epidemiology techniques are being applied to understand transmission of Johne's disease within dairy cattle herds as well as identify which strains predominate in wildlife.

Host responses to persistent Mycobacterium avium subspecies paratuberculosis infection in surgically isolated bovine ileal segments

A lack of appropriate disease models has limited our understanding of the pathogenesis of persistent enteric infections with Mycobacterium avium subsp. paratuberculosis. A model was developed for the controlled delivery of a defined dose of M. avium subsp. paratuberculosis to surgically isolated ileal segments in newborn calves. The stable intestinal segments enabled the characterization of host responses to persistent M. avium subsp. paratuberculosis infections after a 9-month period, including an analysis of local mucosal immune responses relative to an adjacent uninfected intestinal compartment. M. avium subsp. paratuberculosis remained localized at the initial site of intestinal infection and was not detected by PCR in the mesenteric lymph node. M. avium subsp. paratuberculosis-specific T cell proliferative responses included both CD4 and γδ T cell receptor (γδTcR) T cell responses in the draining mesenteric lymph node. The levels of CD8(+) and γδTcR(+) T cells increased significantly (P < 0.05) in the lamina propria, and M. avium subsp. paratuberculosis-specific tumor necrosis factor alpha (TNF-α) and gamma interferon secretion by lamina propria leukocytes was also significantly (P < 0.05) increased. There was a significant (P < 0.05) accumulation of macrophages and dendritic cells (DCs) in the lamina propria, but the expression of mucosal toll-like receptors 1 through 10 was not significantly changed by M. avium subsp. paratuberculosis infection. In conclusion, surgically isolated ileal segments provided a model system for the establishment of a persistent and localized enteric M. avium subsp. paratuberculosis infection in cattle and facilitated the analysis of M. avium subsp. paratuberculosis-specific changes in mucosal leukocyte phenotype and function. The accumulation of DC subpopulations in the lamina propria suggests that further investigation of mucosal DCs may provide insight into host responses to M. avium subsp. paratuberculosis infection and improve vaccine strategies to prevent M. avium subsp. paratuberculosis infection.

Cost-effectiveness of diagnostic strategies to identify Mycobacterium avium subspecies paratuberculosis super-shedder cows in a large dairy herd using antibody enzyme-linked immunosorbent assays, quantitative real-time polymerase chain reaction, and bacterial culture

Diagnostic strategies to detect Mycobacterium avium subsp. paratuberculosis (MAP) super-shedder cows in dairy herds have been minimally studied. The objective of the current study was to compare the cost-effectiveness of strategies for identification of MAP super-shedders on a California dairy herd of 3,577 cows housed in free-stall pens. Eleven strategies that included serum or milk enzyme-linked immunosorbent assay (ELISA), quantitative real-time polymerase chain reaction (qPCR) or culture of environmental samples, pooled or individual cow fecal samples, or combinations thereof were compared. Nineteen super-shedders (0.5%) were identified by qPCR and confirmed by culture as cows shedding ≥10,000 colony forming units (CFU)/g feces (median of 30,000 CFU/g feces). A stratified random sample of the study herd based on qPCR results of fecal pools was the most sensitive (74%) strategy and had the highest cost ($5,398/super-shedder). The reference strategy with the lowest cost ($1,230/super-shedder) and sensitivity (47%) included qPCR testing of fecal samples from ELISA-positive lactating (milk) and nonlactating (serum) cows housed in pens with the highest MAP bioburden. The most cost-effective alternative to the reference was to perform qPCR testing of fecal samples from ELISA-positive cows (milk and serum for milking and dry cows, respectively) for a sensitivity of 68% and cost of $2,226/super-shedder. In conclusion, diagnostic strategies varied in their cost-effectiveness depending on the tests, specimen type, and labor costs. Initial qPCR testing of environmental samples from free-stall pens to target cows in pens with the highest MAP bioburden for further testing can improve the cost-effectiveness of strategies for super-shedder identification.

Evaluation of combined high-efficiency DNA extraction and real-time PCR for detection of Mycobacterium avium subsp. paratuberculosis in subclinically infected dairy cattle: comparison with faecal culture, milk real-time PCR and milk ELISA

Background

Johne’s disease is caused by Mycobacterium avium subsp. paratuberculosis (Map) and it is one of the most important diseases in cattle worldwide. Several laboratory tests for Map detection are available; however, these are limited by inadequate sensitivity and specificity when used in subclinically infected populations. To identify Map shedders in subclinically infected cattle, we used a new, high-yield method for DNA-extraction from Map in faeces combined with quantitative real-time PCR (qPCR) for amplification of the insertion sequence IS900 of Map (HYDEqPCR). Evaluation of HYDEqPCR was carried out in comparison with faecal culture, milk qPCR, and milk enzyme-linked immunosorbent assay (ELISA), on 141 faecal and 91 milk samples, from 141 subclinically infected dairy cattle.

Results

The qPCR proved to be highly sensitive, with a detection limit of 2 IS900 DNA copies/μl in 67 % of the reactions. It also showed 100 % specificity, as determined from 50 Map and non-Map strains, and by the sequencing of qPCR amplicons. The detection limit of HYDEqPCR was 90 Map/g Map-spiked faeces, which corresponds to 2.4 colony forming units/g Map-spiked faeces, with an estimated efficiency of 85 % (±21 %). When tested on the field samples, HYDEqPCR showed 89 % of the samples as positive for Map, whereas faecal culture, milk qPCR, and milk ELISA detected 19 %, 36 % and 1 %, respectively. Fisher’s exact tests only show statistical significance (p ≤0.05) for the correlation between HYDEqPCR and faecal culture. The agreement between HYDEqPCR and milk qPCR and milk ELISA was poor, slight, and non-significant.

Conclusions

This study highlights the advantages of HYDEqPCR for detection of Map in subclinically infected populations, in comparison with faecal culture, milk qPCR and milk ELISA. HYDEqPCR can detect low-level Map shedders that go undetected using these other methods, which will thus underestimate the proportions of Map-shedders in herds. Identification of these shedding animals is extremely important for prevention of the spread of Map infection in an animal population. Due to the relatively high sensitivity and specificity of HYDEqPCR, it can be applied to test for Map at the herd or individual level, regardless of animal age or production stage. HYDEqPCR will allow early detection and control of Map in any population at risk.

Evolution of the bovine TLR gene family and member associations with Mycobacterium avium subspecies paratuberculosis infection

Members of the Toll-like receptor (TLR) gene family occupy key roles in the mammalian innate immune system by functioning as sentries for the detection of invading pathogens, thereafter provoking host innate immune responses. We utilized a custom next-generation sequencing approach and allele-specific genotyping assays to detect and validate 280 biallelic variants across all 10 bovine TLR genes, including 71 nonsynonymous single nucleotide polymorphisms (SNPs) and one putative nonsense SNP. Bayesian haplotype reconstructions and median joining networks revealed haplotype sharing between Bos taurus taurus and Bos taurus indicus breeds at every locus, and specialized beef and dairy breeds could not be differentiated despite an average polymorphism density of 1 marker/158 bp. Collectively, 160 tagSNPs and two tag insertion-deletion mutations (indels) were sufficient to predict 100% of the variation at 280 variable sites for both Bos subspecies and their hybrids, whereas 118 tagSNPs and 1 tagIndel predictively captured 100% of the variation at 235 variable sites for B. t. taurus. Polyphen and SIFT analyses of amino acid (AA) replacements encoded by bovine TLR SNPs indicated that up to 32% of the AA substitutions were expected to impact protein function. Classical and newly developed tests of diversity provide strong support for balancing selection operating on TLR3 and TLR8, and purifying selection acting on TLR10. An investigation of the persistence and continuity of linkage disequilibrium (r²≥0.50) between adjacent variable sites also supported the presence of selection acting on TLR3 and TLR8. A case-control study employing validated variants from bovine TLR genes recognizing bacterial ligands revealed six SNPs potentially eliciting small effects on susceptibility to Mycobacterium avium spp paratuberculosis infection in dairy cattle. The results of this study will broadly impact domestic cattle research by providing the necessary foundation to explore several avenues of bovine translational genomics, and the potential for marker-assisted vaccination.